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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HIV-1 CAPSID IN COMPLEX WITH INHIBITOR BM4
 
Authors :  C. T. Lemke
Date :  20 Mar 12  (Deposition) - 25 Apr 12  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Protein Capsid, Structural Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. T. Lemke, S. Titolo, U. Von Schwedler, N. Goudreau, J. F. Mercier, E. Wardrop, A. M. Faucher, R. Coulombe, S. S. Banik, L. Fader, A. Gagnon S. H. Kawai, J. Rancourt, M. Tremblay, C. Yoakim, B. Simoneau, J. Archambault, W. I. Sundquist, S. W. Mason
Distinct Effects Of Two Hiv-1 Capsid Assembly Inhibitor Families That Bind The Same Site Within The N-Terminal Domain Of The Viral Ca Protein.
J. Virol. V. 86 6643 2012
PubMed-ID: 22496222  |  Reference-DOI: 10.1128/JVI.00493-12
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAG PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 133-278
    Gene: GAG
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
10OE2Ligand/Ion4-{2-[5-(3-CHLOROPHENYL)-1H-PYRAZOL-4-YL]-1-[3-(1H-IMIDAZOL-1-YL)PROPYL]-1H-BENZIMIDAZOL-5-YL}BENZOICACID
20OG2Ligand/Ion3-{5-[3-ETHYL-5-(5-METHYLFURAN-2-YL)-1H-PYRAZOL-1-YL]-1-[(6-OXO-1,6-DIHYDROPYRIDIN-3-YL)METHYL]-1H-BENZIMIDAZOL-2-YL}-4-HYDROXYBENZOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
10OE1Ligand/Ion4-{2-[5-(3-CHLOROPHENYL)-1H-PYRAZOL-4-YL]-1-[3-(1H-IMIDAZOL-1-YL)PROPYL]-1H-BENZIMIDAZOL-5-YL}BENZOICACID
20OG1Ligand/Ion3-{5-[3-ETHYL-5-(5-METHYLFURAN-2-YL)-1H-PYRAZOL-1-YL]-1-[(6-OXO-1,6-DIHYDROPYRIDIN-3-YL)METHYL]-1H-BENZIMIDAZOL-2-YL}-4-HYDROXYBENZOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
10OE1Ligand/Ion4-{2-[5-(3-CHLOROPHENYL)-1H-PYRAZOL-4-YL]-1-[3-(1H-IMIDAZOL-1-YL)PROPYL]-1H-BENZIMIDAZOL-5-YL}BENZOICACID
20OG1Ligand/Ion3-{5-[3-ETHYL-5-(5-METHYLFURAN-2-YL)-1H-PYRAZOL-1-YL]-1-[(6-OXO-1,6-DIHYDROPYRIDIN-3-YL)METHYL]-1H-BENZIMIDAZOL-2-YL}-4-HYDROXYBENZOIC ACID
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
10OE2Ligand/Ion4-{2-[5-(3-CHLOROPHENYL)-1H-PYRAZOL-4-YL]-1-[3-(1H-IMIDAZOL-1-YL)PROPYL]-1H-BENZIMIDAZOL-5-YL}BENZOICACID
20OG2Ligand/Ion3-{5-[3-ETHYL-5-(5-METHYLFURAN-2-YL)-1H-PYRAZOL-1-YL]-1-[(6-OXO-1,6-DIHYDROPYRIDIN-3-YL)METHYL]-1H-BENZIMIDAZOL-2-YL}-4-HYDROXYBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:80 , GLU A:98 , TRP A:117 , HIS A:120 , PRO A:122 , ILE A:124 , ARG A:132 , HOH A:302 , HOH A:304 , HOH A:404 , PRO B:34 , GLU B:35 , ILE B:37 , PRO B:38 , ILE B:135 , ASN B:139BINDING SITE FOR RESIDUE 0OE A 201
2AC2SOFTWAREASN A:21 , VAL A:24 , LYS A:25 , VAL A:27 , GLU A:28 , ALA A:31 , PHE A:32 , SER A:33 , VAL A:59 , HIS A:62 , MET A:66 , LEU A:138 , ILE A:141 , VAL A:142 , TYR A:145 , HOH A:306 , HOH A:352 , HOH A:353 , HOH A:379BINDING SITE FOR RESIDUE 0OG A 202
3AC3SOFTWAREPRO A:34 , GLU A:35 , ILE A:37 , ILE A:135 , ASN A:139 , ASN B:5 , GLN B:7 , GLU B:98 , HIS B:120 , PRO B:122 , ILE B:124 , PRO B:125 , ARG B:132 , HOH B:301BINDING SITE FOR RESIDUE 0OE B 201
4AC4SOFTWAREALA A:14 , ILE A:15 , ASN A:57 , HOH A:323 , VAL B:27 , ALA B:31 , PHE B:32 , SER B:33 , VAL B:36 , VAL B:59 , HIS B:62 , MET B:66 , LEU B:69 , ILE B:141 , VAL B:142 , TYR B:145 , HOH B:302 , HOH B:308 , HOH B:339BINDING SITE FOR RESIDUE 0OG B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E92)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:121 -Pro A:122
2Asn B:121 -Pro B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E92)

(-) Exons   (0, 0)

(no "Exon" information available for 4E92)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains d4e92a_ A: HIV-1 capsid protein                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e92 A   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 146
                                    10        20        30        40        50        60        70        80      ||96       106       116       126       136       146
                                                                                                                 87|                                                    
                                                                                                                  94                                                    


Chain B from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains d4e92b_ B: HIV-1 capsid protein                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e92 B   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 146
                                    10        20        30        40        50        60        70        80      ||96       106       116       126       136       146
                                                                                                                 87|                                                    
                                                                                                                  94
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E92)

(-) Gene Ontology  (50, 62)

Asymmetric Unit(hide GO term definitions)

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  4e92
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  POL_HV1N5 | P12497
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  Q79791_9HIV1 | Q79791
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POL_HV1N5 | P12497: 1a43 1a8o 1afv 1ak4 1aum 1b92 1b9d 1b9f 1baj 1bhl 1bi4 1bis 1biu 1biz 1bl3 1gwp 1hiw 1hyv 1hyz 1itg 1k6y 1m9d 1qs4 1uph 1wjb 1wjd 1wkn 1za9 2b4j 2gol 2gon 2h3f 2h3i 2h3q 2h3v 2h3z 2hmx 2hvp 2itg 2jpr 2jyg 2jyl 2lf4 2lya 2lyb 2m3z 2m8l 2m8n 2m8p 2ont 2pwm 2pwo 2pxr 2x2d 2xde 2xv6 2xxm 3av9 3ava 3avb 3avc 3avf 3avg 3avh 3avi 3avj 3avk 3avl 3avm 3avn 3dik 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 3gv2 3h47 3h4e 3l3u 3l3v 3lpt 3lpu 3lry 3mge 3nf6 3nf7 3nf8 3nf9 3nfa 3p05 3p0a 3s85 3wne 3wnf 3wng 3wnh 4ah9 4ahr 4ahs 4aht 4ahu 4ahv 4coc 4cop 4dga 4dge 4dmn 4e1m 4e1n 4e91 4gvm 4gw6 4id1 4ipy 4jlh 4jmu 4lqw 4nx4 4o0j 4o55 4o5b 4phv 4qnb 4wym 4zhr 5hvp 9hvp
        Q79791_9HIV1 | Q79791: 4e91 4inb
UniProtKB/TrEMBL
        Q79791_9HIV1 | Q79791: 2pxr 3j34 3j3q 3j3y 3j4f 4j93

(-) Related Entries Specified in the PDB File

4e91